Site and sequences simulation under non-homogeneous models. More...

#include <Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h>

Inheritance diagram for bpp::NonHomogeneousSequenceSimulator:

Collaboration diagram for bpp::NonHomogeneousSequenceSimulator:

Public Member Functions
const SubstitutionModelSet *	getSubstitutionModelSet () const
	Get the substitution model associated to this instance. More...

const DiscreteDistribution *	getRateDistribution () const
	Get the rate distribution associated to this instance. More...

const Tree *	getTree () const
	Get the tree associated to this instance. More...

void	enableContinuousRates (bool yn)
	Enable the use of continuous rates instead of discrete rates. More...

The SiteSimulator interface
Site *	simulateSite () const

Site *	simulateSite (size_t ancestralStateIndex) const

Site *	simulateSite (size_t ancestralStateIndex, double rate) const

Site *	simulateSite (double rate) const

std::vector< std::string >	getSequencesNames () const

The DetailedSiteSimulator interface.
RASiteSimulationResult *	dSimulateSite () const
	Get a detailed simulation result for one site. More...

RASiteSimulationResult *	dSimulateSite (size_t ancestralStateIndex) const

RASiteSimulationResult *	dSimulateSite (size_t ancestralStateIndex, double rate) const

RASiteSimulationResult *	dSimulateSite (double rate) const

The SequenceSimulator interface
SiteContainer *	simulate (size_t numberOfSites) const

SiteSimulator and SequenceSimulator interface
const Alphabet *	getAlphabet () const

Functions with rate classes instead of absolute rates.
virtual Site *	simulateSite (size_t ancestralStateIndex, size_t rateClass) const

virtual RASiteSimulationResult *	dSimulateSite (size_t ancestralStateIndex, size_t rateClass) const

Protected Member Functions
size_t	evolve (const SNode *node, size_t initialStateIndex, size_t rateClass) const
	Evolve from an initial state along a branch, knowing the evolutionary rate class. More...

size_t	evolve (const SNode *node, size_t initialStateIndex, double rate) const
	Evolve from an initial state along a branch, knowing the evolutionary rate. More...

void	multipleEvolve (const SNode *node, const std::vector< size_t > &initialStateIndices, const std::vector< size_t > &rateClasses, std::vector< size_t > &finalStates) const
	The same as the evolve(initialState, rateClass) function, but for several sites at a time. More...

SiteContainer *	multipleEvolve (const std::vector< size_t > &initialStates, const std::vector< size_t > &rateClasses) const

void	dEvolve (size_t initialState, double rate, RASiteSimulationResult &rassr) const

The 'Internal' methods.
void	evolveInternal (SNode *node, size_t rateClass) const

void	evolveInternal (SNode *node, double rate) const

void	multipleEvolveInternal (SNode *node, const std::vector< size_t > &rateClasses) const

void	dEvolveInternal (SNode *node, double rate, RASiteSimulationResult &rassr) const

Private Attributes
const SubstitutionModelSet *	modelSet_

const Alphabet *	alphabet_

std::vector< int >	supportedStates_

const DiscreteDistribution *	rate_

const Tree *	templateTree_

TreeTemplate< SNode >	tree_

bool	ownModelSet_

std::vector< SNode * >	leaves_
	This stores once for all all leaves in a given order. This order will be used during site creation. More...

std::vector< std::string >	seqNames_

size_t	nbNodes_

size_t	nbClasses_

size_t	nbStates_

bool	continuousRates_

Stores intermediate results.
	NonHomogeneousSequenceSimulator (const SubstitutionModelSet modelSet, const DiscreteDistribution rate, const Tree *tree) throw (Exception)

	NonHomogeneousSequenceSimulator (const SubstitutionModel model, const DiscreteDistribution rate, const Tree *tree)

virtual	~NonHomogeneousSequenceSimulator ()

	NonHomogeneousSequenceSimulator (const NonHomogeneousSequenceSimulator &nhss)

NonHomogeneousSequenceSimulator &	operator= (const NonHomogeneousSequenceSimulator &nhss)

NonHomogeneousSequenceSimulator *	clone () const

void	init ()
	Init all probabilities. More...

Detailed Description

Site and sequences simulation under non-homogeneous models.

Rate across sites variation is supported, using a DiscreteDistribution object or by specifying explicitely the rate of the sites to simulate.

Definition at line 95 of file NonHomogeneousSequenceSimulator.h.

Constructor & Destructor Documentation

◆ NonHomogeneousSequenceSimulator() [1/3]

NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator	(	const SubstitutionModelSet *	modelSet,
		const DiscreteDistribution *	rate,
		const Tree *	tree
	)
throw	(	Exception
	)

Definition at line 57 of file NonHomogeneousSequenceSimulator.cpp.

Referenced by clone().

◆ NonHomogeneousSequenceSimulator() [2/3]

NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator	(	const SubstitutionModel *	model,
		const DiscreteDistribution *	rate,
		const Tree *	tree
	)

Definition at line 82 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::StateMap::clone(), bpp::SubstitutionModel::clone(), bpp::SubstitutionModelSetTools::createHomogeneousModelSet(), bpp::SubstitutionModel::getFrequencies(), bpp::SubstitutionModel::getStateMap(), init(), modelSet_, and templateTree_.

◆ ~NonHomogeneousSequenceSimulator()

virtual bpp::NonHomogeneousSequenceSimulator::~NonHomogeneousSequenceSimulator ( )

inlinevirtual

Definition at line 141 of file NonHomogeneousSequenceSimulator.h.

References modelSet_, and ownModelSet_.

◆ NonHomogeneousSequenceSimulator() [3/3]

bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator ( const NonHomogeneousSequenceSimulator & nhss )

inline

Definition at line 146 of file NonHomogeneousSequenceSimulator.h.

Member Function Documentation

◆ clone()

NonHomogeneousSequenceSimulator* bpp::NonHomogeneousSequenceSimulator::clone ( ) const

inlinevirtual

Implements bpp::SequenceSimulator.

Definition at line 185 of file NonHomogeneousSequenceSimulator.h.

References NonHomogeneousSequenceSimulator().

◆ dEvolve()

void NonHomogeneousSequenceSimulator::dEvolve	(	size_t	initialState,
		double	rate,
		RASiteSimulationResult &	rassr
	)		const

protected

Definition at line 515 of file NonHomogeneousSequenceSimulator.cpp.

References dEvolveInternal(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::Node::getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), and tree_.

Referenced by dSimulateSite().

◆ dEvolveInternal()

void NonHomogeneousSequenceSimulator::dEvolveInternal	(	SNode *	node,
		double	rate,
		RASiteSimulationResult &	rassr
	)		const

protected

This method uses the states_ variable for saving ancestral states.

Definition at line 528 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::SiteSimulationResult::addNode(), bpp::Node::getDistanceToFather(), bpp::NodeTemplate< NodeInfos >::getFather(), bpp::Node::getId(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::Node::getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), and bpp::Node::hasFather().

Referenced by dEvolve().

◆ dSimulateSite() [1/5]

RASiteSimulationResult * NonHomogeneousSequenceSimulator::dSimulateSite ( ) const

virtual

Get a detailed simulation result for one site.

Returns: A SiteSimulationResult object with all ancestral states for all nodes and branches.

Implements bpp::DetailedSiteSimulator.

Definition at line 300 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::SubstitutionModelSet::getRootFrequencies(), modelSet_, and nbStates_.

Referenced by dSimulateSite().

◆ dSimulateSite() [2/5]

RASiteSimulationResult * NonHomogeneousSequenceSimulator::dSimulateSite ( size_t ancestralStateIndex ) const

virtual

Implements bpp::DetailedSiteSimulator.

Definition at line 322 of file NonHomogeneousSequenceSimulator.cpp.

References continuousRates_, dSimulateSite(), and rate_.

◆ dSimulateSite() [3/5]

RASiteSimulationResult * NonHomogeneousSequenceSimulator::dSimulateSite	(	size_t	ancestralStateIndex,
		double	rate
	)		const

virtual

Implements bpp::DetailedSiteSimulator.

Definition at line 340 of file NonHomogeneousSequenceSimulator.cpp.

References dEvolve(), bpp::SubstitutionModelSet::getAlphabet(), modelSet_, and templateTree_.

◆ dSimulateSite() [4/5]

RASiteSimulationResult * NonHomogeneousSequenceSimulator::dSimulateSite ( double rate ) const

virtual

Implements bpp::DetailedSiteSimulator.

Definition at line 357 of file NonHomogeneousSequenceSimulator.cpp.

References dSimulateSite(), bpp::SubstitutionModelSet::getRootFrequencies(), modelSet_, and nbStates_.

◆ dSimulateSite() [5/5]

RASiteSimulationResult * NonHomogeneousSequenceSimulator::dSimulateSite	(	size_t	ancestralStateIndex,
		size_t	rateClass
	)		const

virtual

Definition at line 350 of file NonHomogeneousSequenceSimulator.cpp.

References dSimulateSite(), and rate_.

◆ enableContinuousRates()

void bpp::NonHomogeneousSequenceSimulator::enableContinuousRates ( bool yn )

inline

Enable the use of continuous rates instead of discrete rates.

To work, the DiscreteDistribution object used should implement the randC method.

Parameters

yn	Tell if we should use continuous rates.

Definition at line 280 of file NonHomogeneousSequenceSimulator.h.

References continuousRates_.

◆ evolve() [1/2]

size_t NonHomogeneousSequenceSimulator::evolve	(	const SNode *	node,
		size_t	initialStateIndex,
		size_t	rateClass
	)		const

protected

Evolve from an initial state along a branch, knowing the evolutionary rate class.

This method is fast since all pijt have been computed in the constructor of the class. This method is used for the implementation of the SiteSimulator interface.

Definition at line 378 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::NodeTemplate< NodeInfos >::getInfos(), and nbStates_.

Referenced by evolveInternal().

◆ evolve() [2/2]

size_t NonHomogeneousSequenceSimulator::evolve	(	const SNode *	node,
		size_t	initialStateIndex,
		double	rate
	)		const

protected

Evolve from an initial state along a branch, knowing the evolutionary rate.

This method is slower than the previous one since exponential terms must be computed. This method is used for the implementation of the SiteSimulator interface.

Definition at line 391 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::Node::getDistanceToFather(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::SubstitutionModel::getPij_t(), nbStates_, and bpp::SubstitutionModel::Pij_t().

◆ evolveInternal() [1/2]

void NonHomogeneousSequenceSimulator::evolveInternal	(	SNode *	node,
		size_t	rateClass
	)		const

protected

This method uses the states_ variable for saving ancestral states.

Definition at line 432 of file NonHomogeneousSequenceSimulator.cpp.

References evolve(), bpp::NodeTemplate< NodeInfos >::getFather(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::Node::getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), and bpp::Node::hasFather().

Referenced by evolveInternal(), and simulateSite().

◆ evolveInternal() [2/2]

void NonHomogeneousSequenceSimulator::evolveInternal	(	SNode *	node,
		double	rate
	)		const

protected

This method uses the states_ variable for saving ancestral states.

Definition at line 448 of file NonHomogeneousSequenceSimulator.cpp.

References evolve(), evolveInternal(), bpp::NodeTemplate< NodeInfos >::getFather(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::Node::getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), and bpp::Node::hasFather().

◆ getAlphabet()

const Alphabet* bpp::NonHomogeneousSequenceSimulator::getAlphabet ( ) const

inlinevirtual

Implements bpp::SequenceSimulator.

Definition at line 240 of file NonHomogeneousSequenceSimulator.h.

References alphabet_.

◆ getRateDistribution()

const DiscreteDistribution* bpp::NonHomogeneousSequenceSimulator::getRateDistribution ( ) const

inline

Get the rate distribution associated to this instance.

Returns: The DiscreteDistribution object associated to this instance.

Definition at line 264 of file NonHomogeneousSequenceSimulator.h.

References rate_.

◆ getSequencesNames()

std::vector<std::string> bpp::NonHomogeneousSequenceSimulator::getSequencesNames ( ) const

inlinevirtual

Implements bpp::SiteSimulator.

Definition at line 210 of file NonHomogeneousSequenceSimulator.h.

References seqNames_.

◆ getSubstitutionModelSet()

const SubstitutionModelSet* bpp::NonHomogeneousSequenceSimulator::getSubstitutionModelSet ( ) const

inline

Get the substitution model associated to this instance.

Returns: The substitution model associated to this instance.

Definition at line 257 of file NonHomogeneousSequenceSimulator.h.

References modelSet_.

Referenced by bpp::HomogeneousSequenceSimulator::getSubstitutionModel().

◆ getTree()

const Tree* bpp::NonHomogeneousSequenceSimulator::getTree ( ) const

inline

Get the tree associated to this instance.

Returns: The Tree object associated to this instance.

Definition at line 271 of file NonHomogeneousSequenceSimulator.h.

References templateTree_.

◆ init()

void NonHomogeneousSequenceSimulator::init ( )

private

Init all probabilities.

Method called by constructors.

Definition at line 108 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::Node::getDistanceToFather(), bpp::Node::getId(), bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::SubstitutionModelSet::getModelForNode(), leaves_, modelSet_, nbClasses_, nbNodes_, nbStates_, rate_, seqNames_, and tree_.

Referenced by NonHomogeneousSequenceSimulator().

◆ multipleEvolve() [1/2]

void NonHomogeneousSequenceSimulator::multipleEvolve	(	const SNode *	node,
		const std::vector< size_t > &	initialStateIndices,
		const std::vector< size_t > &	rateClasses,
		std::vector< size_t > &	finalStates
	)		const

protected

The same as the evolve(initialState, rateClass) function, but for several sites at a time.

This method is used for the implementation of the SequenceSimulator interface.

Definition at line 408 of file NonHomogeneousSequenceSimulator.cpp.

References bpp::NodeTemplate< NodeInfos >::getInfos(), and nbStates_.

Referenced by multipleEvolveInternal(), and simulate().

◆ multipleEvolve() [2/2]

SiteContainer * NonHomogeneousSequenceSimulator::multipleEvolve	(	const std::vector< size_t > &	initialStates,
		const std::vector< size_t > &	rateClasses
	)		const